OKAY! So I solved the problem!
Apparently, if you give the magma stone and enter from crawli's gym, the game teleports you to the route 5 cave entrance, triggering the scene with the powder, skipping the venam cutscene (and bugging if you try to go down while the mountain is neutral).
Seeing as it bugged me that while I entered from crawli's gym, when I returned I ended up on route 5, blocked by lava. after giving up and getting magma drift and went to buy some more great balls in town. I figured I'd reenter from the gym as it was closer, and LO AND BEHOLD, suddenly a new cutscene with Venam triggered, unlocking the event.
TL;DR
So for those with the same problem: continue through until you get magma drift, go back to the the gym and enter a 2nd time!